Metagenomic Analysis of Antibiotic Resistance Genes in the Fecal Microbiome Following Therapeutic and Prophylactic Antibiotic Administration in Dairy Cows

The use of antibiotics in dairy cattle has the potential to stimulate the development and subsequent fecal dissemination of antibiotic resistance genes (ARGs) in bacteria. The objectives were to use metagenomic techniques to evaluate the effect of antibiotic treatment on ARG prevalence in the fecal microbiome of the dairy cow and to determine the temporal excretion pattern of ARGs. Twelve Holstein cows were assigned to one of four antibiotic treatments: control, pirlimycin, ceftiofur, or cephapirin. Fecal samples were collected on d -1, 1, 3, 5, 7, 14, 21, and 28. Samples were freeze-dried and subjected to DNA extraction followed by Illumina paired-end HiSeq sequencing and quantitative polymerase chain reaction (qPCR). Illumina sequences were analyzed using MG-RAST and the Antibiotic Resistance Gene Database (ARDB) via BLAST. Abundance of ampC, ermB, tetO, tetW, and 16S rRNA genes were determined using qPCR. All data were statistically analyzed with PROC GLIMMIX in SAS. Antibiotic treatment resulted in a shift in bacterial cell functions. Sequences associated with 'resistance to antibiotics and toxic compounds' were higher in ceftiofur-treated cows than control cows. Ceftiofur-treated cows had a higher abundance of 𝛽-lactam and multidrug resistance sequences than control cows. There was no effect of treatment or day on fecal tetO and ermB excretion. The relative abundances of tetW and ampC were higher on d 3 post-treatment than d 5 and d 28. In conclusion, antibiotic use in dairy cattle shifted bacterial cell functions and temporarily increased antibiotic resistance in the fecal microbiome.

Name thesis:degree_name

Master of Science

Level thesis:degree_level

masters

Discipline thesis:degree_discipline

Dairy Science

Department dc:contributor.department

Dairy Science

Grantor dc:publisher

Virginia Tech

Year dc:date.issued

2014

Author dc:creator

• Caudle, Lindsey Renee

Chair dc:contributor.committeechair

• Knowlton, Katharine F.

Committee members dc:contributor.committeemember

• Strickland, Michael
• Pruden, Amy
• Akers, Robert Michael

• shotgun metagenomic sequencing
• antibiotic resistance
• dairy cow

Statement dc:rights

• In Copyright

Licence dc:rights.uri

• http://rightsstatements.org/vocab/InC/1.0/

Dc Identifier Other

vt_gsexam:3509

OAI identifier oai:identifier

oai:vtechworks.lib.vt.edu:10919/49676